N. Alcala, T. Jenkins, P. Christe, and S. Vuilleumier, Host shift and cospeciation rate estimation from co-phylogenies, Ecology Letters, vol.75, issue.11, pp.1014-1024, 2017.
DOI : 10.1016/j.tpb.2009.02.003

L. Arvestad, A. Berglund, J. Lagergren, and B. Sennblad, Bayesian gene/species tree reconciliation and orthology analysis using MCMC, Bioinformatics, vol.19, issue.Suppl 1, pp.19-26, 2003.
DOI : 10.1093/bioinformatics/btg1000

URL : https://academic.oup.com/bioinformatics/article-pdf/19/suppl_1/i7/613532/btg1000.pdf

J. A. Balbuena, R. Míguez-lozano, and I. Blasco-costa, PACo: A Novel Procrustes Application to Cophylogenetic Analysis, PLoS ONE, vol.420, issue.4, p.61048, 2013.
DOI : 10.1371/journal.pone.0061048.s002

M. S. Bansal, E. J. Alm, and M. Kellis, Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss, Bioinformatics, vol.449, issue.Suppl. 1, pp.28-283, 2012.
DOI : 10.1038/nature06107

C. Baudet, B. Donati, B. Sinaimeri, P. Crescenzi, C. Gautier et al., Cophylogeny Reconstruction via an Approximate Bayesian Computation, Systematic Biology, vol.73, issue.4, pp.416-431, 2014.
DOI : 10.1016/0022-5193(78)90137-6

URL : https://hal.archives-ouvertes.fr/hal-01092972

M. A. Beaumont, J. Cornuet, J. Marin, R. , and C. P. , Adaptive approximate Bayesian computation, Biometrika, vol.104, issue.6, pp.983-990, 2009.
DOI : 10.1073/pnas.0607208104

URL : https://hal.archives-ouvertes.fr/hal-00280461

M. A. Beaumont, W. Zhang, and D. J. Balding, Approximate bayesian computation in population genetics, Genetics, vol.162, issue.4, pp.2025-2035, 2002.

D. R. Brooks and D. A. Mclennan, Phylogeny, Ecology, and Behavior: A Research Program in Comparative Biology, 1991.

M. A. Charleston, Jungles: a new solution to the host/parasite phylogeny reconciliation problem, Mathematical Biosciences, vol.149, issue.2, pp.191-223, 1998.
DOI : 10.1016/S0025-5564(97)10012-8

M. A. Charleston, Recent Results in Cophylogeny Mapping, Advances in Parasitology, vol.54, pp.303-330, 2003.
DOI : 10.1016/S0065-308X(03)54007-6

M. A. Charleston, TreeMap 3b. https://sites.google.com/site, 2012.

M. A. Charleston and S. L. Perkins, Traversing the tangle: Algorithms and applications for cophylogenetic studies, Journal of Biomedical Informatics, vol.39, issue.1, pp.62-71, 2006.
DOI : 10.1016/j.jbi.2005.08.006

C. Conow, D. Fielder, Y. Ovadia, and R. Libeskind-hadas, Jane: a new tool for the cophylogeny reconstruction problem, Algorithms for Molecular Biology, vol.5, issue.1, pp.1-10, 2010.
DOI : 10.1186/1748-7188-5-16

D. M. De-vienne, T. Giraud, M. , and O. C. , A congruence index for testing topological similarity between trees, Bioinformatics, vol.26, issue.2, pp.3119-3124, 2007.
DOI : 10.1111/j.1463-6409.1997.tb00421.x

D. Vienne, D. M. Giraud, T. Shykoff, and J. A. , When can host shifts produce congruent host and parasite phylogenies? A simulation approach, Journal of Evolutionary Biology, vol.55, issue.4, pp.1428-1438, 2007.
DOI : 10.1111/j.0014-3820.2002.tb00170.x

J. Deng, F. Yu, H. Li, M. Gebiola, Y. Desdevises et al., Cophylogenetic relationships between Anicetus parasitoids (Hymenoptera: Encyrtidae) and their scale insect hosts (Hemiptera: Coccidae), BMC Evolutionary Biology, vol.13, issue.1, p.275, 2013.
DOI : 10.1371/journal.pone.0037268

URL : https://hal.archives-ouvertes.fr/hal-01548299

B. Donati, Graph models and algorithms in (co-)evolutionary contexts, 2014.
URL : https://hal.archives-ouvertes.fr/tel-01095298

B. Donati, C. Baudet, B. Sinaimeri, P. Crescenzi, and M. Sagot, EUCALYPT: efficient tree reconciliation enumerator, Algorithms for Molecular Biology, vol.10, issue.1, p.3, 2015.
DOI : 10.1111/j.1755-0998.2010.02955.x

URL : https://hal.archives-ouvertes.fr/hal-01092977

J. Doyon, V. Ranwez, V. Daubin, and V. Berry, Models, algorithms and programs for phylogeny reconciliation, Briefings in Bioinformatics, vol.5, issue.2, pp.392-400, 2011.
DOI : 10.1186/1748-7188-5-16

URL : https://hal.archives-ouvertes.fr/lirmm-00825041

J. Doyon, C. Scornavacca, K. Y. Gorbunov, G. J. Szöllosi, V. Ranwez et al., An Efficient Algorithm for Gene/Species Trees Parsimonious Reconciliation with Losses, Duplications and Transfers, RECOMB International Workshop on Comparative Genomics, pp.93-108, 2011.
DOI : 10.1089/cmb.1997.4.177

URL : https://hal.archives-ouvertes.fr/lirmm-00818889

B. Drinkwater, A. Qiao, and M. A. Charleston, WiSPA: A new approach for dealing with widespread parasitism. arXiv preprint, 2016.

M. Escudero, Phylogenetic congruence of parasitic smut fungi (Anthracoidea, Anthracoideaceae) and their host plants (Carex, Cyperaceae): Cospeciation or host-shift speciation?, American Journal of Botany, vol.102, issue.7, pp.1108-1114, 2015.
DOI : 10.3732/ajb.1500130

S. Gómez-acevedo, L. Rico-arce, A. Delgado-salinas, S. Magallón, and L. E. Eguiarte, Neotropical mutualism between Acacia and Pseudomyrmex: Phylogeny and divergence times, Molecular Phylogenetics and Evolution, vol.56, issue.1, pp.393-408, 2010.
DOI : 10.1016/j.ympev.2010.03.018

P. Górecki, O. Eulenstein, and J. And-tiuryn, Unrooted Tree Reconciliation: A Unified Approach, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.10, issue.2, pp.522-536, 2013.
DOI : 10.1109/TCBB.2013.22

M. S. Hafner and S. A. Nadler, Phylogenetic trees support the coevolution of parasites and their hosts, Nature, vol.332, issue.6161, pp.332258-259, 1988.
DOI : 10.1038/332258a0

M. T. Hallett and J. Lagergren, Efficient algorithms for lateral gene transfer problems, Proceedings of the fifth annual international conference on Computational biology , RECOMB '01, pp.149-156, 2001.
DOI : 10.1145/369133.369188

S. A. Hendricks, M. E. Flannery, and G. S. Spicer, Cophylogeny of quill mites from the genus Syringophilopsis (Acari: Syringophilidae) and their North American passerine hosts, The Journal of Parasitology, issue.5, pp.99827-834, 2013.

B. Holland, D. Penny, and M. Hendy, Outgroup Misplacement and Phylogenetic Inaccuracy Under a Molecular Clock???A Simulation Study, Systematic Biology, vol.52, issue.2, pp.229-238, 2003.
DOI : 10.1080/10635150390192771

K. Hommola, J. E. Smith, Y. Qiu, and W. R. Gilks, A Permutation Test of Host-Parasite Cospeciation, Molecular Biology and Evolution, vol.10, issue.3, pp.1457-1468, 2009.
DOI : 10.1093/molbev/msm092

J. P. Huelsenbeck, B. Rannala, and B. Larget, A BAYESIAN FRAMEWORK FOR THE ANALYSIS OF COSPECIATION, Evolution, vol.10, issue.2, pp.352-364, 2000.
DOI : 10.1007/BF00160154

J. P. Huelsenbeck, B. Rannala, Y. , and Z. , STATISTICAL TESTS OF HOST-PARASITE COSPECIATION, Evolution, vol.213, issue.2, pp.410-419, 1997.
DOI : 10.1098/rstb.1925.0002

A. L. Hughes and R. Friedman, Evolutionary Diversification of Protein-Coding Genes of Hantaviruses, Molecular Biology and Evolution, vol.17, issue.10, pp.1558-1568, 2000.
DOI : 10.1093/oxfordjournals.molbev.a026254

J. Hughes, M. Kennedy, K. P. Johnson, R. L. Palma, P. et al., Multiple Cophylogenetic Analyses Reveal Frequent Cospeciation between Pelecaniform Birds and Pectinopygus Lice, Systematic Biology, vol.51, issue.2, pp.232-251, 2007.
DOI : 10.1080/10635150290102339

URL : http://sysbio.oxfordjournals.org/content/56/2/232.full.pdf

J. Hugot, Primates and Their Pinworm Parasites: The Cameron Hypothesis Revisited, Systematic Biology, vol.48, issue.3, pp.523-546, 1999.
DOI : 10.1080/106351599260120

J. Hugot, New evidence for hystricognath rodent monophyly from the phylogeny of their pinworms. Tangled trees: Phylogeny, cospeciation and coevolution, pp.144-173, 2003.

A. P. Jackson and P. Andrew, The Effect of Paralogous Lineages on the Application of Reconciliation Analysis by Cophylogeny Mapping, Systematic Biology, vol.17, issue.1, pp.127-145, 2005.
DOI : 10.1093/oxfordjournals.molbev.a026389

A. P. Jackson and M. A. Charleston, A Cophylogenetic Perspective of RNA-Virus Evolution, Molecular Biology and Evolution, vol.21, issue.1, pp.45-57, 2004.
DOI : 10.1093/molbev/msg232

E. Jacox, C. Chauve, G. J. Szöllosi, Y. Ponty, and C. Scornavacca, ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony: Table 1., Bioinformatics, vol.2014, issue.13, pp.322056-2058, 2016.
DOI : 10.1109/TCBB.2010.14

URL : https://academic.oup.com/bioinformatics/article-pdf/32/13/2056/16920517/btw105.pdf

G. Jansen, K. Vepsäläinen, and R. Savolainen, A phylogenetic test of the parasite-host associations between Maculinea butterflies (Lepidoptera: Lycaenidae) and Myrmica ants (Hymenoptera: Formicidae), European Journal of Entomology, vol.48, issue.1, pp.53-62, 2011.
DOI : 10.1163/157075608X383683

D. S. Johnson, M. Yannakakis, and C. H. Papadimitriou, On generating all maximal independent sets, Information Processing Letters, vol.27, issue.3, pp.119-123, 1988.
DOI : 10.1016/0020-0190(88)90065-8

W. A. Kosters and J. F. Laros, Metrics for Mining Multisets, Research and Development in Intelligent systems XXIV, pp.293-303, 2008.
DOI : 10.1007/978-1-84800-094-0_22

P. Legendre, Y. Desdevises, and E. Bazin, A Statistical Test for Host???Parasite Coevolution, Systematic Biology, vol.51, issue.2, pp.217-234, 2002.
DOI : 10.1080/10635150252899734

R. Libeskind-hadas, Y. Wu, M. S. Bansal, and M. Kellis, Pareto-optimal phylogenetic tree reconciliation, Bioinformatics, vol.8, issue.12, pp.30-87, 2014.
DOI : 10.1109/TCBB.2010.14

URL : https://academic.oup.com/bioinformatics/article-pdf/30/12/i87/17347240/btu289.pdf

A. Martínez-aquino, F. S. Ceccarelli, L. E. Eguiarte, E. Vázquez-domínguez, G. P. De-león et al., Do the Historical Biogeography and Evolutionary History of the Digenean Margotrema spp. across Central Mexico Mirror Those of Their Freshwater Fish Hosts (Goodeinae)?, PLoS ONE, vol.35, issue.5, p.101700, 2014.
DOI : 10.1371/journal.pone.0101700.s003

M. J. Mcleish and S. Van-noort, Codivergence and multiple host species use by fig wasp populations of the Ficus pollination mutualism, BMC Evolutionary Biology, vol.12, issue.1, p.1, 2012.
DOI : 10.1080/10635150490264987

M. Mendlová, Y. Desdevises, K. Civá?ová, A. Pariselle, and A. ?imková, Monogeneans of West African Cichlid Fish: Evolution and Cophylogenetic Interactions, PLoS ONE, vol.56, issue.5, p.37268, 2012.
DOI : 10.1371/journal.pone.0037268.t005

D. Merkle and M. Middendorf, Reconstruction of the cophylogenetic history of related phylogenetic trees with divergence timing information, Theory in Biosciences, vol.123, issue.4, pp.277-299, 2005.
DOI : 10.1016/j.thbio.2005.01.003

D. Merkle, M. Middendorf, and N. Wieseke, A parameter-adaptive dynamic programming approach for inferring cophylogenies, BMC Bioinformatics, vol.11, issue.Suppl 1, p.60, 2010.
DOI : 10.1186/1471-2105-11-S1-S60

E. A. Murray, A. E. Carmichael, and J. M. Heraty, Ancient host shifts followed by host conservatism in a group of ant parasitoids, Proceedings of the Royal Society B: Biological Sciences, vol.106, issue.32, p.28020130495, 1759.
DOI : 10.1073/pnas.0811087106

M. Nei and S. Kumar, Molecular Evolution and Phylogenetics, 2000.

K. Nemirov, A. Vaheri, and A. Plyusnin, Hantaviruses: co-evolution with natural hosts, Recent Res. Devel. Virol, vol.6, pp.201-228, 2004.

Y. Ovadia, D. Fielder, C. Conow, and R. Libeskind-hadas, The Cophylogeny Reconstruction Problem Is NP-Complete, Journal of Computational Biology, vol.18, issue.1, pp.59-65, 2011.
DOI : 10.1089/cmb.2009.0240

DOI : 10.1016/0020-7519(93)90041-V

R. D. Page and M. A. Charleston, Trees within trees: phylogeny and historical associations, Trends in Ecology & Evolution, vol.13, issue.9, pp.356-359, 1998.
DOI : 10.1016/S0169-5347(98)01438-4

URL : http://taxonomy.zoology.gla.ac.uk/rod/papers/tree.pdf

A. Paterson, R. D. Gray, D. H. Clayton, M. , and J. , Host-parasite co-speciation, host switching, and missing the boat, Host-parasite evolution: General principles and avian models, pp.236-250, 1997.

A. Paterson and R. Poulin, Have chondracanthid copepods co-speciated with their teleost hosts? Systematic Parasitology, pp.79-85, 1999.

A. M. Paterson and J. Banks, Analytical approaches to measuring cospeciation of host and parasites: through a glass, darkly, International Journal for Parasitology, vol.31, issue.9, pp.311012-1022, 2001.
DOI : 10.1016/S0020-7519(01)00199-0

A. M. Paterson, R. L. Palma, and R. D. Gray, Drowning on arrival, missing the boat, and x-events: How likely are sorting events, Tangled trees: Phylogeny, Cospeciation, and Coevolution, pp.287-309, 2003.

S. L. Perkins and J. Schall, A Molecular Phylogeny of Malarial Parasites Recovered from Cytochrome b Gene Sequences, The Journal of Parasitology, vol.88, issue.5, pp.972-978, 2002.
DOI : 10.2307/3285540

A. Plyusnin and S. Morzunov, Virus Evolution and Genetic Diversity of Hantaviruses and Their Rodent Hosts, Hantaviruses, pp.47-75, 2001.
DOI : 10.1007/978-3-642-56753-7_4

Y. Qiu, J. Lee, B. A. Whitlock, F. Bernasconi-quadroni, and O. Dombrovska, Was the ANITA Rooting of the Angiosperm Phylogeny Affected by Long-Branch Attraction?, Molecular Biology and Evolution, vol.18, issue.9, pp.1745-1753, 2001.
DOI : 10.1093/nar/24.6.1008

C. Ramsden, E. C. Holmes, and M. A. Charleston, Hantavirus Evolution in Relation to Its Rodent and Insectivore Hosts: No Evidence for Codivergence, Molecular Biology and Evolution, vol.30, issue.2, pp.143-153, 2008.
DOI : 10.1007/s11262-004-5625-2

G. Refrégier, L. Gac, M. Jabbour, F. Widmer, A. Shykoff et al., Cophylogeny of the anther smut fungi and their caryophyllaceous hosts: Prevalence of host shifts and importance of delimiting parasite species for inferring cospeciation, BMC Evolutionary Biology, vol.8, issue.1, p.100, 2008.
DOI : 10.1186/1471-2148-8-100

I. Ricci, M. Valzano, U. Ulissi, S. Epis, A. Cappelli et al., Symbiotic control of mosquito borne disease, Pathogens and Global Health, vol.5, issue.12, pp.380-385, 2012.
DOI : 10.1371/journal.pntd.0001440

F. Ronquist, Parsimony analysis of coevolving species associations, Tangled trees: Phylogeny, Cospeciation, and Coevolution, pp.22-64, 2003.

F. Ronquist and S. Nylin, Process and Pattern in the Evolution of Species Associations, Systematic Zoology, vol.39, issue.4, pp.323-344, 1990.
DOI : 10.2307/2992354

M. Rosenblueth, L. Sayavedra, H. Sámano-sánchez, A. Roth, and E. Martínez-romero, Evolutionary relationships of flavobacterial and enterobacterial endosymbionts with their scale insect hosts (Hemiptera: Coccoidea), Journal of Evolutionary Biology, vol.84, issue.11, pp.252357-2368, 2012.
DOI : 10.1266/ggs.84.57

M. J. Sanderson and H. B. Shaffer, Troubleshooting Molecular Phylogenetic Analyses, Annual Review of Ecology and Systematics, vol.33, issue.1, pp.49-72, 2002.
DOI : 10.1146/annurev.ecolsys.33.010802.150509

P. Simões, Diversity and dynamics of Wolbachia-host associations in arthropods from the Society archipelago, French Polynesia, 2012.

P. Simões, G. Mialdea, D. Reiss, M. Sagot, C. et al., Wolbachia detection: an assessment of standard PCR Protocols, Molecular Ecology Resources, vol.265, issue.3, pp.567-572, 2011.
DOI : 10.1098/rspb.1998.0324

J. Stavrinides and D. S. Guttman, Mosaic Evolution of the Severe Acute Respiratory Syndrome Coronavirus, Journal of Virology, vol.78, issue.1, pp.76-82, 2004.
DOI : 10.1128/JVI.78.1.76-82.2004

M. Stolzer, L. Han, M. Xu, D. Sathaye, B. Vernot et al., Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees, Bioinformatics, vol.17, issue.18, pp.28-409, 2012.
DOI : 10.1093/bioinformatics/17.9.821

M. Stolzer, L. Han, M. Xu, D. Sathaye, B. Vernot et al., Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees, Bioinformatics, vol.17, issue.18, pp.28-409, 2012.
DOI : 10.1093/bioinformatics/17.9.821

URL : https://academic.oup.com/bioinformatics/article-pdf/28/18/i409/16906592/bts386.pdf

D. L. Swofford, G. J. Olsen, P. J. Waddell, and D. M. Hillis, Phylogenetic inference, Molecular Systematics, pp.407-514, 1996.

G. J. Szöllosi, W. Rosikiewicz, B. Boussau, E. Tannier, and V. Daubin, Efficient exploration of the space of reconciled gene trees, Systematic Biology, issue.6, pp.62901-912, 2013.

G. J. Szöllosi, E. Tannier, V. Daubin, and B. Boussau, The Inference of Gene Trees with Species Trees, Systematic Biology, vol.17, issue.Web Server issue, pp.42-62, 2015.
DOI : 10.1093/bioinformatics/17.9.821

J. N. Thompson, The Coevolutionary Process, 1994.
DOI : 10.7208/chicago/9780226797670.001.0001

A. Tofigh, M. Hallett, and J. And-lagergren, Simultaneous Identification of Duplications and Lateral Gene Transfers, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.8, issue.2, pp.517-535, 2011.
DOI : 10.1109/TCBB.2010.14

L. Urbini, B. Sinaimeri, C. Matias, and M. Sagot, Robustness of the Parsimonious Reconciliation Method in Cophylogeny, International Conference on Algorithms for Computational Biology (AlCoB), pp.119-130, 2016.
DOI : 10.1109/TCBB.2010.14

URL : https://hal.archives-ouvertes.fr/hal-01349773

L. Urbini, B. Sinaimeri, C. Matias, and M. Sagot, Exploring the robustness of the parsimonious reconciliation method in host-symbiont cophylogeny, IEEE/ACM Trans. Comput. Biology Bioinform, 2017.

M. P. Vanhove, A. Pariselle, M. Van-steenberge, J. A. Raeymaekers, P. I. Hablützel et al., Hidden biodiversity in an ancient lake: phylogenetic congruence between Lake Tanganyika tropheine cichlids and their monogenean flatworm parasites, Scientific Reports, vol.111, issue.1, p.13669, 2015.
DOI : 10.1007/s00436-012-3052-1

E. Viale, I. Martinez-sanudo, J. Brown, M. Simonato, V. Girolami et al., Pattern of association between endemic Hawaiian fruit flies (Diptera, Tephritidae) and their symbiotic bacteria: Evidence of cospeciation events and proposal of ???Candidatus Stammerula trupaneae???, Molecular Phylogenetics and Evolution, vol.90, pp.67-79, 2015.
DOI : 10.1016/j.ympev.2015.04.025

J. D. Weckstein, Biogeography Explains Cophylogenetic Patterns in Toucan Chewing Lice, Systematic Biology, vol.14, issue.1, pp.154-164, 2004.
DOI : 10.1111/j.1096-0031.1998.tb00330.x

Z. Wei and A. Jousset, Plant Breeding Goes Microbial, Trends in Plant Science, vol.22, issue.7, pp.555-558, 2017.
DOI : 10.1016/j.tplants.2017.05.009

URL : http://www.cell.com/article/S1360138517301115/pdf

N. Wieseke, T. Hartmann, M. Bernt, and M. Middendorf, Cophylogenetic Reconciliation with ILP, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.12, issue.6, pp.1227-1235, 2015.
DOI : 10.1109/TCBB.2015.2430336